The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny

Globe artichoke (Cynara cardunculus var. scolymus) is an out-crossing, perennial, multi-use crop species that is grown worldwide and belongs to the Compositae, one of the most successful Angiosperm families. We describe the first genome sequence of globe artichoke. The assembly, comprising of 13,588 scaffolds covering 725 of the 1,084 Mb genome, was generated using ~133-fold Illumina sequencing data and encodes 26,889 predicted genes. Re-sequencing (30×) of globe artichoke and cultivated cardoon (C. cardunculus var. altilis) parental genotypes and low-coverage (0.5 to 1×) genotyping-by-sequencing of 163 F(1) individuals resulted in 73% of the assembled genome being anchored in 2,178 genetic bins ordered along 17 chromosomal pseudomolecules. This was achieved using a novel pipeline, SOILoCo (Scaffold Ordering by Imputation with Low Coverage), to detect heterozygous regions and assign parental haplotypes with low sequencing read depth and of unknown phase. SOILoCo provides a powerful tool for de novo genome analysis of outcrossing species. Our data will enable genome-scale analyses of evolutionary processes among crops, weeds, and wild species within and beyond the Compositae, and will facilitate the identification of economically important genes from related species

Cure indicators and prevalence by stage at diagnosis for breast and colorectal cancer patients: A population‐based study in Italy

People alive many years after breast (BC) or colorectal cancer (CRC) diagnoses are increasing. This paper aimed to estimate the indicators of cancer cure and complete prevalence for Italian patients with BC and CRC by stage and age. A total of 31 Italian Cancer Registries (47% of the population) data until 2017 were included. Mixture cure models allowed estimation of net survival (NS); cure fraction (CF); time to cure (TTC, 5-year conditional NS >95%); cure prevalence (who will not die of cancer); and already cured (prevalent patients living longer than TTC). 2.6% of all Italian women (806,410) were alive in 2018 after BC and 88% will not die of BC. For those diagnosed in 2010, CF was 73%, 99% when diagnosed at stage I, 81% at stage II, and 36% at stages III-IV. For all stages combined, TTC was >10 years under 45 and over 65 years and for women with advanced stages, but <= 1 year for all BC patients at stage I. The proportion of already cured prevalent BC women was 75% (94% at stage I). Prevalent CRC cases were 422,407 (0.7% of the Italian population), 90% will not die of CRC. For CRC patients, CF was 56%, 92% at stage I, 71% at stage II, and 35% at stages III-IV. TTC was <= 10 years for all age groups and stages. Already cured were 59% of all prevalent CRC patients (93% at stage I). Cancer cure indicators by stage may contribute to appropriate follow-up in the years after diagnosis, thus avoiding patients' discrimination

Clinical features and outcomes of elderly hospitalised patients with chronic obstructive pulmonary disease, heart failure or both

Background and objective: Chronic obstructive pulmonary disease (COPD) and heart failure (HF) mutually increase the risk of being present in the same patient, especially if older. Whether or not this coexistence may be associated with a worse prognosis is debated. Therefore, employing data derived from the REPOSI register, we evaluated the clinical features and outcomes in a population of elderly patients admitted to internal medicine wards and having COPD, HF or COPD + HF. Methods: We measured socio-demographic and anthropometric characteristics, severity and prevalence of comorbidities, clinical and laboratory features during hospitalization, mood disorders, functional independence, drug prescriptions and discharge destination. The primary study outcome was the risk of death. Results: We considered 2,343 elderly hospitalized patients (median age 81 years), of whom 1,154 (49%) had COPD, 813 (35%) HF, and 376 (16%) COPD + HF. Patients with COPD + HF had different characteristics than those with COPD or HF, such as a higher prevalence of previous hospitalizations, comorbidities (especially chronic kidney disease), higher respiratory rate at admission and number of prescribed drugs. Patients with COPD + HF (hazard ratio HR 1.74, 95% confidence intervals CI 1.16-2.61) and patients with dementia (HR 1.75, 95% CI 1.06-2.90) had a higher risk of death at one year. The Kaplan-Meier curves showed a higher mortality risk in the group of patients with COPD + HF for all causes (p = 0.010), respiratory causes (p = 0.006), cardiovascular causes (p = 0.046) and respiratory plus cardiovascular causes (p = 0.009). Conclusion: In this real-life cohort of hospitalized elderly patients, the coexistence of COPD and HF significantly worsened prognosis at one year. This finding may help to better define the care needs of this population

Mycorrhizal Inoculation Improves Plant Growth and Yield of Micropropagated Early Globe Artichoke under Field Conditions

The micropropagation appears to be a valid alternative method for the production of large-scale, phenotypically homogeneous, and disease-free plants, particularly for spring globe artichoke genotypes. Nevertheless, micropropagated plants have some problems during the acclimatization in field environments. The inoculation with arbuscular mycorrhizal fungi appeared to overcome the transplanting stress. Therefore, a comparison was drawn between the field performances of different vegetative propagation techniques (micropropagated/mycorrhized and offshoots cultivation) of early globe artichoke clones over two growing seasons. The micropropagation/mycorrhization appeared to deliver a better field performance in terms of both plant growth and productivity traits as compared with offshoots cultivated. In particular, the micropopagated/mycorrhized plants exhibited the highest vegetative growth values than the offshoots of the cultivated ones, such as the plant height and the main floral stem length. The micropopagated/mycorrhized plants were also more productive, exceeding the head yield of offshoots cultivated ones by about 63%. However, the micropopagated/mycorrhized plants accumulated almost a month late on the first harvest respect to offshoots cultivated ones. Our data also showed that the effects of the new proposed propagation method were genotype- and season-dependent. Accordingly, some plant growth and productivity traits showed significant ‘propagation method × genotype’ and ‘propagation method × growing season’ interaction. This study revealed that the micropropagation, as well as the mycorrhization, could represent an efficient and sustainable cropping system to reintroduce and increase the productivity of autochthons landraces

Mycorrhizal Inoculation Improves Plant Growth and Yield of Micropropagated Early Globe Artichoke under Field Conditions

The micropropagation appears to be a valid alternative method for the production of large-scale, phenotypically homogeneous, and disease-free plants, particularly for spring globe artichoke genotypes. Nevertheless, micropropagated plants have some problems during the acclimatization in field environments. The inoculation with arbuscular mycorrhizal fungi appeared to overcome the transplanting stress. Therefore, a comparison was drawn between the field performances of different vegetative propagation techniques (micropropagated/mycorrhized and offshoots cultivation) of early globe artichoke clones over two growing seasons. The micropropagation/mycorrhization appeared to deliver a better field performance in terms of both plant growth and productivity traits as compared with offshoots cultivated. In particular, the micropopagated/mycorrhized plants exhibited the highest vegetative growth values than the offshoots of the cultivated ones, such as the plant height and the main floral stem length. The micropopagated/mycorrhized plants were also more productive, exceeding the head yield of offshoots cultivated ones by about 63%. However, the micropopagated/mycorrhized plants accumulated almost a month late on the first harvest respect to offshoots cultivated ones. Our data also showed that the effects of the new proposed propagation method were genotype- and season-dependent. Accordingly, some plant growth and productivity traits showed significant ‘propagation method × genotype’ and ‘propagation method × growing season’ interaction. This study revealed that the micropropagation, as well as the mycorrhization, could represent an efficient and sustainable cropping system to reintroduce and increase the productivity of autochthons landraces

In vitro micropropagation and mycorrhizal treatment influences the polyphenols content profile of globe artichoke under field conditions

The commercial importance of plant tissue culture has grown in recent years, reflecting its application to vegetative propagation, disease elimination, plant improvement and the production of polyphenols. The level of polyphenols present in plant tissue is influenced by crop genotype, the growing environment, the crop management regime and the post-harvest processing practice. Globe artichoke is a significant component of the Mediterranean Basin agricultural economy, and is rich in polyphenols (phenolic acids and flavones). Most commercially grown plants are derived via vegetative propagation, with its attendant risk of pathogen build-up. Here, a comparison was drawn between the polyphenol profiles of conventionally propagated and micropropagated/mycorrhized globe artichoke plants. Micropropagation/mycorrhization appeared to deliver a higher content of caffeoylquinic acids. The accumulation of these compounds, along with luteolin and its derivatives, was not season-dependent. Luteolin aglycone was accumulated preferentially in the conventionally propagated plants. Overall, it appeared that micropropagation/mycorrhization enhanced the accumulation of polyphenols